DNA encoded libraries are now routinely employed as part of reductionist lead generation campaigns in Pharma. The large number of compounds contained in many of these libraries (> 1 Billion) when combined with modest hit rates (0.1%) often result in thousands of potential hits. The compounds are generated as large combinatorial mixtures and “selected” for affinity to the target of interest. As a result the first step in hit triage is to resynthesize the compounds of interest without the DNA tag and confirm that the observed affinity for the target translates into the desired functional activity. Here we present experimental protocols and informatics methods that can estimate the affinity of the hits in the DNA encoded library mixture, thus enabling the incorporation of a ligand efficiency estimate into the decision making process for compound resynthesis.